The Network
Workbench (NWB) tool(v0.8.0 release) is a network analysis,
modeling, and visualization toolkit for biomedical, social science, and physics
research. It is a standalone desktop application requiring Java 1.4+ JRE. The tool installs
and runs on multiple platforms (see section 3.1 for details).

It uses the Cyberinfrastructure
Shell (CIShell) to integrate
various datasets and algorithms. Although CIShell is developed using Java, it
can integrate algorithms developed in other programming languages such as
FORTRAN, C, and C++.

2.Downloading, Installing and
Uninstalling

Download the NWB tool v0.8.0 and make
sure to save the download as a jar file.

To install the NWB tool, simply double
click the jar file, or run the command line java -jar nwb-installer_0.8.0.jar or java -jar nwb-web-nstaller_0.8.0.jar

To uninstall the NWB tool, run Uninstall NWB from
your operating system program menu or run uninstaller.jar (in NWB Install
Directory/Uninstaller).

3.What’s
New

3.1.Full
Installer vs. Web Installer

In this release we continue providing a full installer nwb-installer_0.8.0.jar (size 62.5MB) that can run on Windows
XP, Linux x86, and Mac OS X (PowerPC and Intel).

·To
run the NWB tool on Windows Vista, your only option is to
download and run the web installer.

·All
non-Java based algorithms, especially all algorithms written in FORTRAN (see
table 1 in section 4.2) are NOT pre-compiled on Solaris and Windows Vista
platforms.
So they may not run properly on those platforms. We will fix this problem in
the next release.

3.2.New
Algorithm Plug-ins and Improvements:

·Added
several plug-ins to support a prototype of loading an ISI file, extracting a
co-authorship network, and updating the co-authorship network by merging nodes (authors
with different names). A tutorial on this topic will be available soon.

·Added a
plug-in to integrate GUESS – a graph exploration
system. Note: This plug-in works on Mac
and Linux but does not work on Windows. We will try to fix the problem before
the next release.

nwb_announce@googlegroups.com
is a very low traffic mailing list for
announcements regarding the NWB project and software releases, mostly release
notes and important updates.

nwb_helpdesk@googlegroups.com
is the main mailing list for the NWB community.
Subscribe to this list to participate in the project, ask for help, report
bugs (temporary solution), talk about NWB-related matters.

nwb_dev@googlegroups.com
is NWB development mailing list. Subscribe to this
list and take part in the NWB development, talk about NWB-development related
matters or to keep up to date with NWB development.

The tool supports viewing and saving of plain text files
generated by algorithms.

The tool can load and process an edge
list with two columns (*.edge) but can’t save as an edge list.

For detailed information about the above file formats, please visit the NWB
Community Wiki.

4.2.Algorithms

The tool provides over 60
network analysis, modeling, and visualization algorithms. They are developed
using FORTRAN, Java, Perl, ocaml, etc. Detailed algorithm descriptions are
available at the NWB
Community Wiki. Here is the complete algorithm list in the v0.8.0 release.

The tool provides a set of converters and a conversion
service that automatically transforms data from one format to another. The
conversion service tries to find a chain of converters that can transform the
input data format to one that an algorithm can accept. Figure 1 shows the core
conversion graph supported by the NWB tool v0.8.0 release. Figure 2 shows a
detailed conversion graph including many converters that

··References and Documentations of
Algorithms: When
a user selects an algorithm from the menu, an acknowledgement appears in the
console. The acknowledgement contains the original authors of the algorithm,
the developers, the integrators, a reference, and the URL to the reference if
available. Furthermore, the acknowledgement includes a URL to the algorithm
description at the NWB community wiki website at https://nwb.slis.indiana.edu/community.

·Scheduler: The Scheduler allows users to monitor the progress of
running algorithms and to stop/pause/resume running algorithms that implement
the scheduling API. A scheduler tester algorithm is provided to demonstrate the
capabilities of the scheduler.

·InvokeGnuplot through the NWB tool:
the tool provides a plug-in that can invoke Gnuplot
--- a portable
command-line driven interactive data and function plotting utility. This plug-in works on Windows,
Linux, and Mac. To make the plug-in work on Linux and Mac, the tool
requires a working installation of the Gnuplot package. It has been packaged in
the NWB tool for Windows installation.

·Graph Analysis Toolkit is a nice tool for getting the
insight of your datasets. It provides such rich information as number of nodes,
number of edges, the density of a graph, directed vs. undirected graph, whether
the graph has self-loops and/or duplicate edges, whether there’s a potential
error when a graph claims to be an undirected graph but has duplicate edges or
self loops, whether the graph has weakly connected components, whether the
graph has strongly connected components, etc.

5.Known Issues

This list covers some of the known problems with NWB Tool
v0.3.0. Please read this before reporting any new bugs.

··Algorithm Performance: Algorithms developed in FORTRAN
are more scalable and efficient when comparing to Java-based implementations.
They can generate and deal with large networks with over 1,000,000 nodes, which
Java algorithms generally cannot.

··Visualization Algorithms: The Kamada-Kawai and Fruchterman
Reingold algorithms cannot handle networks with 1000 nodes because the algorithms themselves have high complexity. It
takes excessive time for JUNG-based visualization
algorithms, including Circular and Spring Layout, to visualize a graph
with over 1000 nodes and they cannot handle a graph with over 5000 nodes in
general.

··Stop a Running Algorithm: Although the new scheduler allows users to stop/pause/resume
a running algorithm, only algorithms written in Java that implement the ProgressTrackable
interface can be controlled by the scheduler. So far, only a few algorithms
integrated in the tool implement this interface. A scheduler tester algorithm
under FileŕTest is provided to demonstrate
the capabilities of the scheduler.

6.Icons

The NWB tool uses the following icons to represent different
datasets: